5VLO | pdb_00005vlo

The structure of human CamKII with bound inhibitor

PDB DOI: https://doi.org/10.2210/pdb5VLO/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-25 Released: 2017-08-23
Deposition Author(s): Somoza, J.R., Villasenor, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.188 (DCC)
R-Value Observed:
0.184 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibitors of CamKII

Somoza, T.J., Villasenor, A.G.

To be published.

Macromolecule Content

Total Structure Weight: 70.32 kDa
Atom Count: 5,137
Modeled Residue Count: 583
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium/calmodulin-dependent protein kinase type II subunit delta	A, B	302	Homo sapiens	Mutation(s): 0 Gene Names: CAMK2D, CAMKD EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13557 (Homo sapiens) Explore Q13557 Go to UniProtKB: Q13557
PHAROS: Q13557 GTEx: ENSG00000145349
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13557
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9EJ Query on 9EJ Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide C₂₈ H₃₄ N₈ O₂ S BKSPZDICBZFRLV-MBSDFSHPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
DTT Query on DTT Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.188 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.473	α = 90
b = 67.546	β = 94.111
c = 85.45	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
EPMR	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-08-23

Deposition Author(s):

Villasenor, A.G.

Revision History (Full details and data files)

Version 1.0: 2017-08-23
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection
Version 1.2: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.